Abstract

In recent papers, there has been a lively exchange concerning theories for enzyme catalysis, especially the role of protein dynamics/pre-chemistry conformational changes in the catalytic cycle of enzymes. Of particular interest is the notion that substrate-induced conformational changes that assemble the polymerase active site prior to chemistry are required for DNA synthesis and impact fidelity (i.e., substrate specificity). High-resolution crystal structures of DNA polymerase β representing intermediates of substrate complexes prior to the chemical step are available. These structures indicate that conformational adjustments in both the protein and substrates must occur to achieve the requisite geometry of the reactive participants for catalysis. We discuss computational and kinetic methods to examine possible conformational change pathways that lead from the observed crystal structure intermediates to the final structures poised for chemistry. The results, as well as kinetic data from site-directed mutagenesis studies, are consistent with models requiring pre-chemistry conformational adjustments in order to achieve high fidelity DNA synthesis. Thus, substrate-induced conformational changes that assemble the polymerase active site prior to chemistry contribute to DNA synthesis even when they do not represent actual rate-determining steps for chemistry.

Editor’s Note: This paper and papers by Mulholland AJ, Roitberg AE, Tuñón I (doi:10.​1007/​s00214-012-1286-8) and Ram Prasad B, Kamerlin SCL, Florián J, Warshel A (doi:10.​1007/​s00214-012-1288-6) document and discuss contrasting outlooks on the questions of pre-chemistry and catalysis in DNA polymerase. All authors were initially provided with one another's manuscripts, at which point opportunities to make revisions were offered, and finally Mulholland, Roitberg, and Tuñón were given the 'last word' on the revised manuscripts in their role as commentators. The editors of TCA hope that this discussion will illuminate key issues affecting ongoing work in this area.